c.600 -750 CE Culture St. Marinos, probably from Syria, was a monk, kicked out of his order when he was thought to have fathered a child with a woman out of wedlock. He was later allowed to return to his order and helped raise the boy. Upon his death he was found to have female anatomy.
1025 CE Medical - This paper on the history of estrogen therapies notes that pills made from concentrated, evaporated urine of men or of women were used to treat various hypogonadic maladies (though it does not state it was used to for cross gender therapies).
After 1286 Culture French philosopher, Kalonymus ben Kalonymus, wrote poetry describing her longing to be female despite her anatomical circumstances. Further copies of her poetry here.
1394 Legal Eleanor Rykener, a London embroiderist and tapster, was put on trial for prostitution and along with a client, sodomy. The court treated her as a man but she lived and worked as a woman. The outcome of her case is unknown.
1431 Legal Jeanne d’Arc was convicted and executed for witchcraft and heresy, charges supported both by the voices she heard which she attributed to God and saints, as well as her crossdressing in male soldier’s garb.
A collection of resources on Medieval Trans History can be found at Nico Mara-McKay et al.'s Bibliography of Medieval Trans Studies